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[go-friends] [go-discuss] Announcement: three new relationship types to be added to core GO file

Erick Antezana erick.antezana at gmail.com
Mon May 13 06:36:06 PDT 2013


Hi  Jane,

thanks for the test file. I can confirm that syntactically there are no
issues (it can be digested by my pipeline  ;-) )

however, I was wondering whether these set of new relationships would
support the "modelling"  of variants of the mitotic cell cycle (e.g.
endocycle -> endoreduplication)?

cheers,
Erick


On 10 May 2013 15:02, Robinson, Peter <peter.robinson at charite.de> wrote:

> What are, then, the parts of puberty? ****
>
> ** **
>
> It would be nice to see a bunch of examples of the intended use cases of
> the new relations. I would imagine that****
>
> ** **
>
> processA happensDuring process****
>
> would be most common (e.g., anaphase happensDuring Mitosis)****
>
> ** **
>
> In this case it is not incorrect to have happensDuring be a SubPropertyOf
> part_of ****
>
> ** **
>
> Therefore, it would be important to know if there are range/domain
> restrictions on happensDuring.****
>
> ** **
>
> -Peter****
>
> ** **
>
> Dr. med. Peter N. Robinson, MSc.****
>
> Professor of Medical Genomics
> Institut für Medizinische Genetik und Humangenetik
> Charité - Universitätsmedizin Berlin
> Augustenburger Platz 1
> 13353 Berlin
> Germany
> +4930 450566006
> Mobile: 0160 93769872
> peter.robinson at charite.de
> http://compbio.charite.de
> http://www.human-phenotype-ontology.org
> Introduction to Bio-Ontologies:
> http://www.crcpress.com/product/isbn/9781439836651****
>
> ** **
>
> *Von:* go-friends-bounces at lists.stanford.edu [mailto:
> go-friends-bounces at lists.stanford.edu] *Im Auftrag von *David
> Osumi-Sutherland
> *Gesendet:* Freitag, 10. Mai 2013 13:30
> *An:* Alan Ruttenberg
> *Cc:* Jane Lomax; go-discuss at lists.stanford.edu; Phillip Lord; Chris
> Mungall; go-friends at mailman.stanford.edu
> *Betreff:* Re: [go-friends] [go-discuss] Announcement: three new
> relationship types to be added to core GO file****
>
> ** **
>
> ** **
>
> On 10 May 2013, at 10/May/2013 12:12:19, Alan Ruttenberg wrote:****
>
>
>
> ****
>
>
>
> On Friday, May 10, 2013, Phillip Lord wrote:
>
> ****
>
>
>
> Like "Wearing long trousers" happens_during "puberty", but is not
> part_of it.
>
> Phil****
>
> ** **
>
> Nice example...
>
>
> ****
>
> Not like. (Or bug)****
>
> ** **
>
> name: happens_during****
>
> ...****
>
> is_a: BFO:0000050 ! part of****
>
> ** **
>
> bug.  Should be fixed ASAP.  This probably comes from ro as I just checked
> in ro-edit.owl and found it had accidentally gotten into there (in OWLish:
> happens_during SubPropertyOf part_of). I have deleted this axiom. ****
>
> ** **
>
> - David****
>
>
>
> ****
>
> -Alan****
>
> ** **
>
> ** **
>
> ** **
>
>  ****
>
>
>
> Chris Mungall <cjmungall at lbl.gov> writes:
> > We're currently separating out cell cycle phases from biological
> processes
> > proper. We don't consider the processes to be part of the stage. We
> would use
> > the happens_during relation to connect processes to stages.
> >
> > This is all consistent with release 2 of the Basic Formal Ontology
> (BFO), the
> > relation can be defined in terms of a chain of the ''occupies
> spatiotemporal
> > region' relation with part_of between occurrents.
> >
> > On May 7, 2013, at 9:14 AM, Alan Ruttenberg wrote:
> >
> >> How does happens_during differ from part_of?
> >>
> >> Thanks,
> >> Alan
> >>
> >>
> >> On Tue, May 7, 2013 at 8:50 AM, Jane Lomax <jane at ebi.ac.uk> wrote:
> >> Dear GO friends - we will be adding three new relationships to this
> core GO file:
> >>
> >> go.obo     http://purl.obolibrary.org/obo/go.obo
> >> go.owl     http://purl.obolibrary.org/obo/go.owl
> >>
> >> For more information about the content of these and other files, please
> see our beta ontology downloads page:
> >>
> >> http://beta.geneontology.org/page/download-ontology
> >>
> >> Note that this file is equivalent to these legacy files:
> >>
> >>
> ftp://ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology.1_2.obo
> >> ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo
> >>
> >> so these files will be affected too.
> >>
> >> The relationships are starts_with, ends_with and happens_during. Their
> >> definitions from the OBO relations ontology are listed below.
> >>
> >> We'll start adding these to the file in 2 weeks, 21 May 2013. Let us
> know if you have any questions.
> >>
> >> many thanks,
> >>
> >> GO ontology editors
> >>
> >>
> >>
> >> From: http://code.google.com/p/obo-relations/
> >> [Typedef]
> >> id: RO:0002224
> >> name: starts with
> >> def: "x starts with y if and only if x has part y and the time point at
> >> which x starts is equivalent to the time point at which y starts.
> Formally:
> >> ?(y) = ?(x) ? ?(y) < ?(x), where ? is a function that maps a process to
> a
> >> start point, and ? is a function that maps a process to an end point."
> []
> >> property_value: IAO:0000112 "Every insulin receptor signaling pathway
> starts
> >> with the binding of a ligand to the insulin receptor" xsd:string
> >> property_value: IAO:0000114 IAO:0000125
> >> property_value: IAO:0000118 "started by" xsd:string
> >> is_transitive: true
> >> is_a: BFO:0000051 ! has part
> >> is_a: RO:0002222 ! temporally related to
> >> inverse_of: RO:0002223 ! starts
> >>
> >> [Typedef]
> >> id: RO:0002230
> >> name: ends with
> >> def: "x ends with y if and only if x has part y and the time point at
> which
> >> x ends is equivalent to the time point at which y ends. Formally: ?(y) >
> >> ?(x) ? ?(y) = ?(x), where ? is a function that maps a process to a start
> >> point, and ? is a function that maps a process to an end point." []
> >> property_value: IAO:0000114 IAO:0000125
> >> property_value: IAO:0000118 "finished by" xsd:string
> >> is_transitive: true
> >> is_a: BFO:0000051 ! has part
> >> is_a: RO:0002222 ! temporally related to
> >>
> >> [Typedef]
> >> id: RO:0002092
> >> name: happens_during
> >> comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with
> >> start(X)) AND (end(X) before_or_simultaneous_with end(Y))
> >> property_value: IAO:0000118 "d" xsd:string
> >> property_value: IAO:0000118 "during" xsd:string
> >> is_transitive: true
> >> is_a: BFO:0000050 ! part of
> >> is_a: RO:0002093 ! ends_d>
> _______________________________________________
> > go-friends mailing list
> > go-friends at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/go-friends
>
> --
> Phillip Lord,                           Phone: +44 (0) 191 222 7827
> Lecturer in Bioinformatics,             Email:
> phillip.lord at newcastle.ac.uk
> School of Computing Science,
> http://homepages.cs.ncl.ac.uk/phillip.lord
> Room 914 Claremont Tower,               skype: russet_apples
> Newcastle University,                   twitter: phillord
> NE1 7RU****
>
> _______________________________________________
> go-friends mailing list
> go-friends at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/go-friends****
>
> ** **
>
> David Osumi-Sutherland, PhD****
>
> Ontologist at FlyBase & Virtual Fly Brain****
>
> Department of Genetics, University of Cambridge,****
>
> Downing Street, Cambridge, CB2 3EH, UK****
>
> Tel: +44 (0)1223 333 963, Fax: +44 (0)1223 766 732****
>
> http://www.virtualflybrain.org****
>
> ** **
>
> ** **
>
> ** **
>
> _______________________________________________
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